Messiah
by BlazingSun01
Summary: When the beams struck, everything turned red. The messiah had awoken and flames shall threaten the world. In which Lysandre was successful in controlling Ash and Greninja, not too canon divergent.


**goddamnit why hasn't anyone written fanfics about this au, now I gotta contribute with my shitty writing skills, smh**

 **this is drama bc of lysandre bc hes a dramatic evil dorito.**

 **Disclaimer: I do not own Pokemon, that belongs to Satoshi Tajiri, the Pokemon Company. honestly, it would be worse if I owned it.**

 _I won't let you!_

Ash felt rage, hot and boiling. Red like the energy engulfing him.

"You are the guide for the chosen ones," Lysandre answered.

"That's not what we are!"

The rage grew, unnaturally hot. He screamed in pain as it grew along with Greninja's cries.

Everything was _red._

His control was slipping. He felt rage–no– _hatred_ at something. What disturbed him was that it wasn't Lysandre he was angry at.

 _Humans are filthy_.

His screams grew louder. _Make it stop,_ please _._

 _This world must be_ reborn.

Greninja screeched. His pokemon howled as they struggled to get free. "Pika pi!" Pikachu cried out.

 _This world is imperfect and it needs to be cleansed._

"Stop it, please!" Alain pleaded.

" _I… hate this world,"_ Ash didn't realize that he spoke. Lysandre smirked, triumphant.

"Ash, no!" Alain shouted.

"You shall lead us to victory," Lysandre smiled.

" _I hate the humans in it,_ " Ash radiated the red hue of the Zygarde rampaging in Lumiose City. With a roar perfectly in sync, Greninja's eyes glowed as a storm of water started to form.

"By dawn, nothing will live," Lysandre gloated, ignoring Pikachu's glare.

Alain looked at the scene in horror. He brought this, he _helped_ this man and people suffered because of it. _Ash_ is suffering because of it.

The bonds released the two, Greninja's form changed once more with Ash beside them.

"Pika Pika pi!" Pikachu called but to no avail, Ash couldn't hear him and continued to head to Lysandre's side, Greninja at his heels.

"See, Ash can understand it," Lysandre leered. "Why can't you?"

Alain backed away, a sickened feeling rushing through him. It was too unnatural, the way Ash carried himself (there was no confidence, it looked forced, as if he was attached to strings), the way his eyes looked (too malicious, angry, red). "What have you _done_?"

Lysandre laid a hand on Ash's shoulder, causing his pokemon to cry out in outrage. "I made him see the light. Zygarde sees it, and soon the other one will."

The dark haired boy swallowed, a hand reaching for Charizard's pokeball.

"Ash, deal with him," Lysandre ordered. He clicked a machine on his head, a backpack like machine hovered and latched onto his back as well. A disk turned into a gauntlet and enveloped his hand.

Ash Greninja's stance changed, knees bent and webbed hands reaching to their thigh.

"Charizard, come out!" The pokemon roared as they came out, mega stone gleaming.

"Water shuriken!" Ash commanded, reaching his back much like Greninja, who hurled it straight at Charizard.

"Dodge it!" Charizard leaped into the sky. _'I won't be able to win like this, I have to bring him back.'_ Alain thought. ' _It's my fault he's like this._ '

"Cut!" Greninja leapt into the air, a flash of blue in their hands as kunai formed.

"Dragon claw!" Green claws formed and clashes against the shurikens. Strike after strike, both pokemon moved furiously.

Then both pokemon leapt back, Charizard hovering while Greninja landed in front of Ash.

"Aerial Ace!" Limbs gleamed as they struck. A kick at their stomach, a strike at the face.

"Water shuriken!" Greninja leapt back and shurikens crashed into Charizard, making it roar in pain.

Alain glanced over, Lysandre had that smirk on his face. His blood boiled. Was the man amused? Amused by the fact that Ash was under his control? Amused at the destruction he had wrought upon Kalos?

"Charizard!" A finger pressed to the keystone on his bracelet. "Respond to my heart, keystone! Surpass evolution, mega evolution!"

Charizard roared as the stone around their neck glowed along with the keystone. Blue flames erupted around the illuminated pokemon and the familiar symbol burst in front of them.

"Water shuriken!" Ash shouted, reaching for his back as did Greninja. The large shuriken hurtled towards them.

"Dodge it!" Alain yelled. Charizard flew up.

But Ash had expected that. "Aerial Ace!" A glowing limb crashed down on the dragon's head and it pitched towards the ground and crashed down with a loud thud, dust flew everywhere.

"Charizard!"

–

"Liepard! Shadow Claw!"

"Druddigon, Dragon Claw!"

Clembot glanced upwards. "Heliolisk, Flash!"

A bright light blinded the two pokemon, sending the Liepard crashing into the dragon.

"Luxray, Wild Charge!" Clemont ordered. The Luxray charged at the Druddigon, sending it into the wall.

"Chespin, Pin Needle! Bunnelby, Mud Shot!"

Orange energy gathered at Bunnelby's ears that turned to mud. Chespin's spikes glowed green and fired pins, both attacks meeting their target in an explosion.

"Liepard!" Bryony cried out, the green haired woman watching the dust clear away, revealing their hurt pokemon.

"Return!" Red light gathered the pokemon into their respective pokeballs. Metal roped circled around their waist and pinned their arms to their sides.

They hung at the entrance.

"H-hey!"

"Let me go!"

Clembot looked on. "Capture complete."

"Nice work, Clembot!" Clemont smiled.

"This is all your fault!" Bryony hissed at her companion.

"It's yours!" Aliana argued.

Zygarde, Squishy, roared, drawing their attention. They were wrapped in roots above the red Zygarde and struggling to break free.

–

At the tower, red light gathered in front of a machine at the scientist's command. A crimson beam shot towards its target.

A blonde child with her Dedenne looked cried out. The green Zygarde, her _friend_ , glowed an ominous scarlet like their friend. "Squishy!"

A Mega Blaziken rushed and grabbed her has roots flew at her.

"Young lady! Why have you come here?" Blaziken Mask asked.

She panted, everything seemed so _red_. "Squishy… is about to lose."

A final screech, panic flooded through the child as quickly as the light seemed to overtake them echoed, tortured and _pleading_.

Her friend begged for mercy.

Bonnie wailed as the red vanished. They were so _angry_. Scorching heat seemed to pound at her head.

"Pull yourself together, Bonnie!" Her father shouted.

But it was as if she couldn't hear him. She keened louder, hands clutching her temples.

"Squishy… What happened to you?"

–

The pudgy man in goggles and red, Xerosic, chuckled. "A success."

–

Charizard was fine. A couple bruises but nothing they couldn't shake off.

"Lysandre," An excited voice announced, voices distorted as if it was from a machine. "We are in control of the other Zygarde."

Their leader smirked at this. He had both Zygarde and the boy and his Greninja.

Alain choked. "They have Zygarde?"

"With them in our hands as well as the boy, world peace shall soon be achieved," Lysandre said.

"This isn't peace!" Alain countered. "You are hurting both people and pokemon!"

"And what do you know?" Lysandre sneered. "You are a child, not fully aware of the evils of the world."

 _A dark sky above a ruined city. Lysandre and his scientists each had a box in hand._

"A long time ago, I wanted to save people as well from their suffering and extended a helping hand."

Alain gasped as Lysandre continued his tale. "The people were happy, but that was only at the start! They took advantage of that kindness and kept demanding more. They loudly proclaimed their rights. My helping hand made them arrogant."

"Those are the humans you desired to protect," Lysandre declared. "They are selfish and greedy and have corrupted this world. This world must be reborn from the ashes of the former one."

A fist clenched at Alain's side. _I believe in the Alain I got to know!_ He glanced at Lysandre's side, Ash was scowling, but it was different. It wasn't the passionate fury he normally had, but a simmering rage, the fires dull. It felt _wrong._

He had to this. For Chespie, who's current fate was unknown. For Mairin, his friend who he swore to help save her Chespin. For Ash, who's suffering because of his actions.

"Director," Alain paused. "No, Lysandre, I will not allow you to destroy this world. There are people and pokemon I wish to protect."

He raised his fist, blue eyes blazing like the flames of his Mega Charizard. "I will stop you here, right now!"

"A shame, you're a good trainer, Alain, yet you chose the wrong side." Lysandre sighed and pointed at Alain. "Ash, eliminate him."

"Water Shuriken!" Ash yelled. The shuriken headed towards Alain.

Charizard leapt in front of their trainer, taking the water attack head on and grunted in pain. Alain sweated, Ash Greninja seemed more powerful, the manic look in both trainer and pokemon eyes startled him.

"Ash, listen to me!" Alain urged. "Snap out of it!"

Ash barely seemed to acknowledge him, his red filled eyes, if one observed carefully, seemed slightly dazed and out of focus. Greninja's eyes seemed blank like their trainer's.

"Do you really think you can reach him?" Lysandre questioned, amusement creeping into his voice. "Mega Evolution energy cannot be shaken off so easily."

Charizard roared, wings expanded. "It might be so," Alain answered. "But I'm not giving up!"

–

A helicopter flew under the red evening sky. "Over there!" Mairin pointed at the labs.

–

The doors opened for a woman with purple hair. Celosia marched in.

"Oh?" The blue haired woman took notice of her fellow admin. "You're back. How is Lumoise?"

"It's a festival of plants," She responded. "It's a shame you had to stay here."

"Mable," A grunt called, directing the two women's attentions to a screen. "A news helicopter is approaching us."

"A news helicopter?" Celosia asked.

Mable glanced over at her colleague. "You know what to do, right? Politely show our guests around."

–

Flare grunts laid scattered on the floor of Prism Tower.

Clemont typed in a code. _4-1-0-6_. A beep signaled the code being denied.

"As I thought, the locking code had been overwritten," He said.

"Please leave it to me!" Clembot exclaimed. Its arm manifested a plug and pushed it in the outlet. A series of number codes ran through Clembot's eyes.

"Analyzing… Analyzing…"

–

Bonnie, Blaziken Mask, and Mega Blaziken looked upon the carnage that Zygarde had wrought. The legendary pokemon moved through the broken city, roots following it.

–

"Charizard, Flamethrower!"

"Dodge it!"

The Greninja leapt nimbly upwards. Ash reaches for his back once more. "Water shuriken!"

From their back, Greninja shot a large shuriken towards them.

"Block it!" Alain commanded. Charizard's wings were brought in front of the pokemon and shielding it from much of the damage.

"Pika Pi!" Pikachu, who Alain forgot about, shouted at Ash, electricity gathering but the bonds suppressed them.

"Cut!" A flurry of attacks met Charizard.

"Dragon Claw!" Green energy met the attack in a clash of sparks.

"Flamethrower, up close!" Charizard's maw opened, blue flames burst directly at Greninja. Ash staggered, clutching his stomach and heaving. For a second, Alain wondered if Ash's eyes flashed blue momentarily, but it was just his imagination.

He hesitated, and Ash recovered quickly. "Water Shuriken!" He reached at his sides along with Greninja, blue shurikens striking Charizard.

Alain gritted his teeth. "Ash, say something! You're still in there, aren't you!"

But Ash had remained despondent, eyes cool and unnerving.

"Charizard, Thunder Punch!" Electricity danced in Charizard's claw as it charged towards Greninja.

"Water Shuriken!" Greninja met each blow with precision, however Charizard got a blow in.

Ash grunted as Greninja skidded backwards, both clutching their side.

"This is the potential of Mega Evolution," Lysandre gloated. "An ability that pokemon had forgotten after being tamed. When a pokemon unleashes that fighting instinct, it gains a new power!"

"You're wrong!" Alain argued. "Mega evolution is about–"

"Only the winner decides that," Lysandre cut him off.

"Water Shuriken!" A large shuriken aimed at Charizard.

Zygarde moved through the city, red as the skies above them.

–

Bonnie followed them, breathing heavily as she tried to catch up.

A hand caught her wrist and she turned. Blaziken Mask.

"Wait up!" The masked hero commanded.

"Let me go, I need to get to Squishy!" Bonnie shouted, worry clear in her eyes.

"What can you do?" Blaziken Mask asked.

"I'm going to save Squishy!" Her eyes were filled with anguish and determination. "I promised them that I would not leave them!"

"Dedenne…" Her pokemon wimpered.

He stared at her for a few seconds before she clearly made up her mind and yanked her hand back. "Let go of me!"

"Bonnie!" He cried out as his daughter ran after the enraged pokemon.

–

"Lock-Lifting process complete," Clembot said.

His gym was a bathed in a red light. Grunts manned the stations and screens and turned when they heard the door unlock.

"Who are you?"

"I am the leader of the Lumoise Gym, Clemont!" He declared.

"And I am the substitute Gym leader, Clembot!" Clembot announced, voice almost inaudible from its low battery.

Clemont looked forwards. "Clembot."

"Got it," Clembot's eyes glowed as it scouted out using heat vision.

"There are three enemies, one in the back," Clembot answered. "The one in the back is controlling the machine with similar activity as the Zygarde outside."

Clemont sucked in a breath. "The Control System."

"If you stop them, I might be able to hack into the main system and suspend it."

"Alright!" Clemont pointed to the grunts. "Electric Terrain!"

Luxray let out a field of electricity at the grunts. The grunts cried out before crumpling to the ground.

"Clembot, now!"

"Yes!" Clembot charged off.

"What's all the commotion?" A voice called out. A scientist, different in appearance from the grunts, appeared from the back, hardly shocked at his fallen comrades.

"Well, well, it seems we have an intruder," He said. "What are you doing here?"

"You're controlling Zygarde with that system, aren't you?"

"Yes, it's the fruit of my invention!" The scientist exclaimed.

Before Clemont could retort, a loud crash echoed throughout the room, the tower seemed to shake a little. Xerosic glanced upwards, amused. "My, My, they are really being noisy."

"What's going on?" Clemont asked.

"Oh, just those two boys. Lysandre must be having so much fun."

"What are you talking about?"

Xerosic smirked. "Do you really think that this is the only machine here that can control using Mega Evolution energy?"

Clemont gaped. "W-what?"

He looked thoughtful. "I believe Lysandre had it. He wanted to use it on someone, something about a boy and a Greninja."

The gym leader sharply caught his breath. " _Ash_."

Xerosic glanced over at him, some sinister glee in his expression, the red lights of the room seemed more ominous. "Oh ho, you know him? A friend perhaps?"

"What did you do to him?!" Clemont demanded.

"Oh, _I_ didn't do anything," Xerosic taunted. " _Lysandre_ did. The boy is nothing more than his puppet now."

"You're lying!" Clemont shouted. "Ash wouldn't let himself be controlled!"

"But that same energy can control the likes of Zygarde," Xerosic rebutted with a conceding tone. "Do you really think the little messiah can break free of that?"

"Don't you _dare_ speak of him like that!" Clemont hissed. "Ash isn't some tool for you to use!"

"Hit a nerve, did I?" Xerosic mused. "Well, my invention truly did a number on him."

"Something that destroys a city and controls both pokemon and people cannot be an invention!" Clemont argued.

The Flare Scientist's goggles flashed. "And what do you know?"

"Inventions are meant to help people and pokemon," He answered, voice laced with fury and conviction.

The man pulled out two pokeballs. "Do you really think you can change things?" He tossed them almost nonchalantly, a Malamar and a Crobat.

"I _know_ I can!" A smile filled with determination.

"Crobat, Air Slash! Malamar, Psycho Cut!" The four winged bat and the squid-like pokemon both released their respective slashes.

"Chespin, Pin Missile!" Clembot watched as both inventors called out their moves while it scurried past them.

The robot had a job to do.

–

"Charizard, Thunder Punch!" The dragon charged up a claw filled with electricity and struck the Greninja.

"Aerial ace!" A right arm blocked the incoming punch.

Lysandre looked upon both pokemon, both panting. "Do you really think there's hope for this world?"

"No matter what happened in the past," Alain said. "That's still no excuse to just destroy everything!"

"Only the winner of the fight has any say," The Flare leader retorted. "Look at the state of your pokemon."

Charizard had taken heavy damage from Greninja. Numerous cuts and bruises littered their scaly hide, the blue flames that once bursted from their mouth was dimmer. His other pokemon lacked the power that Mega Charizard had, but the dragon looked like they were about to collapse.

Greninja on the other hand, while not in a terribly injured condition, suffered burns from both Thunder punches and Flamethrowers. Ash himself looked worse for the wear, but he looked fine.

"It seemed that I should finish you off, I have much better things to do," He decided.

"What do you mean by that?" Alain asked.

"Ash, finish him," Lysandre intoned.

For the first time since Lysandre took control, Ash said something other than the name of a move.

"Yes, sir."

The two words chilled Alain, he wished he never spoke at all. The expressive voice Ash once had became brusque and even. There was still the slightest bit of emotions, however that was clearly expressed in his red eyes directed at his enemy. This was unnatural. They boy in front of him couldn't be Ash.

A hand directed towards Alain and Charizard. "Water Shuriken!" The voice tinged with fury. His arm reached for his back much like Greninja and raised it, water whipped around them as the shuriken began to spin, streaks of orange in the whirlpool.

 _This is bad._

At their current height and with the tower's current stability, a Blast Burn could collapse some of the tower. They were on a ledge, not giving too much room unlike with the stadium.

He had to hope that Charizard could withstand the impact.

The attack charged up into a golden shuriken hurled straight at both boy and pokemon. Charizard shifted so they were in front of Alain. The shuriken loomed closer and closer; a move like that could kill him.

Alain braced himself, but a boom resounded; a beam struck and intercepted the giant shuriken.

A woman stepped out of the smoke, a houndoom–mega– trailed behind her.

Alain gaped. "You are…"

"Let's stop this, Lysandre," She said.

Malva, member of Team Flare and the Elite Four, had arrived.

Omake: Replacement-

"Well that worked out," Lysandre commented. Ash was lowered to the ground along with Greninja.

"Aw damnit," Alain groaned. "A heel-face turn?"

"Uhm, no? It's Face-heel turn, get it right," Lysandre sighed.

"What difference is there–"

"I'm gonna fight someone!" Ash shouted, fists pumped.

"Hold on," Lysandre pulled out something from his coat.

It was a pink boa.

"You gotta be fab to roll with us," The Flare leader explained.

"Seriously?" Alain deadpanned.

Ash eyed Alain critically as he wrapped the boa around his neck. "Yeah, no wonder you aren't considered an official Team Flare member."

Alain frowned. "What's that supposed to mean?"

Ash pointed to Alain's pants. "Have you _seen_ that horror show? Those pants are bad and you should feel bad."

Lysandre nodded sagely. "It's true."

"You can't just insult my pants, that's just rude."

Ash flung the boa over his shoulder. "Watch me."

"I'm so proud," Lysandre said.

Alain looked exasperated. "I don't even know what I'm doing here anymore." Charizard nodded.

"You know what this means, Alain?" Ash smirked and then pointed at him. "You've been replaced~"

"YOU'RE NOT EVEN IN TEAM FLARE, ASH!"

Lysandre tossed Ash some glasses, a copy of his. "And now he is, I'm promoting you." He leaned in. "Hurl these to the ground when you lose a battle."

Ash placed them on. "Sweet!"

"What even is this?" He groaned. "I'm _done."_

Pikachu probably let out a string of pika curses. Who knows with pokemon.

"You're just jealous~" Ash taunted.

"I will literally choke you with that scarf," Alain threatened.

"It's a _boa_ , and try it, I bet you can't even do it," Ash smirked.

"Well, at least I _won_ the league"

Ash let loose a roar of fury and tackled Alain to the ground.

"I thought you were cool with that, Ash!" Alain yelled.

"ASH IS FUCKING PISSED!" He shouted and punched Alain several times. The two children were engaged in a fistfight.

Lysandre looked at the scene. "Should we stop them?"

Greninja shrugged, pulling out popcorn from nowhere.

Inspiration:

( scribblekin . tumblr post/147437466621/nihilistgirlfriend-replied-to-your-post ) check them out yoo

 **(A/N)**

 **holy shit do you know how _long_ this took? I haven't watched a majority of the pokemon** **anime and I cri im not even a good writer but I gotta contribute to this idea and I can't write fight scenes**.

 **i love the idea of lysandre taking control of ash and greninja so much because a) it's a cool idea b) angst potential c) he got kidnapped and crucified so that's a plus d) im a slut for mind controlled characters fighting their friends, especially the main characters (i like seeing them getting rescues for once)**

 **for once, im probably gonna finish a fic since im not reckless and charging in this time. if you know my track record, it's pretty surprising, but I was motivated enough to write 3,000 words so I giess that's better.**


End file.
